scholarly journals Computer Vision, Machine Learning, and the Promise of Phenomics in Ecology and Evolutionary Biology

2021 ◽  
Vol 9 ◽  
Author(s):  
Moritz D. Lürig ◽  
Seth Donoughe ◽  
Erik I. Svensson ◽  
Arthur Porto ◽  
Masahito Tsuboi
Keyword(s):  
Machine Learning ◽  
Computer Vision ◽  
Evolutionary Biology ◽  
Digital Images ◽  
Phenotypic Diversity ◽  
Image Data ◽  
Comprehensive Method ◽  
Biological Phenomena ◽  
Level Data ◽  
Wide Range

For centuries, ecologists and evolutionary biologists have used images such as drawings, paintings and photographs to record and quantify the shapes and patterns of life. With the advent of digital imaging, biologists continue to collect image data at an ever-increasing rate. This immense body of data provides insight into a wide range of biological phenomena, including phenotypic diversity, population dynamics, mechanisms of divergence and adaptation, and evolutionary change. However, the rate of image acquisition frequently outpaces our capacity to manually extract meaningful information from images. Moreover, manual image analysis is low-throughput, difficult to reproduce, and typically measures only a few traits at a time. This has proven to be an impediment to the growing field of phenomics – the study of many phenotypic dimensions together. Computer vision (CV), the automated extraction and processing of information from digital images, provides the opportunity to alleviate this longstanding analytical bottleneck. In this review, we illustrate the capabilities of CV as an efficient and comprehensive method to collect phenomic data in ecological and evolutionary research. First, we briefly review phenomics, arguing that ecologists and evolutionary biologists can effectively capture phenomic-level data by taking pictures and analyzing them using CV. Next we describe the primary types of image-based data, review CV approaches for extracting them (including techniques that entail machine learning and others that do not), and identify the most common hurdles and pitfalls. Finally, we highlight recent successful implementations and promising future applications of CV in the study of phenotypes. In anticipation that CV will become a basic component of the biologist’s toolkit, our review is intended as an entry point for ecologists and evolutionary biologists that are interested in extracting phenotypic information from digital images.

scholarly journals Computer vision, machine learning, and the promise of phenomics in ecology and evolutionary biology

2020 ◽  
Author(s):  
Moritz Lürig ◽  
Seth Donoughe ◽  
Erik Svensson ◽  
Arthur Porto ◽  
Masahito Tsuboi
Keyword(s):  
Machine Learning ◽  
Computer Vision ◽  
Image Analysis ◽  
Evolutionary Biology ◽  
Image Data ◽  
Phenotypic Trait ◽  
Biological Phenomena ◽  
Level Data ◽  
Wide Range ◽  
Insight Into

For centuries, ecologists and evolutionary biologists have used images such as drawings, paintings, and photographs to record and quantify the shapes and patterns of life. With the advent of digital imaging, biologists continue to collect image data at an ever-increasing rate. This immense body of data provides insight into a wide range of biological phenomena, including phenotypic trait diversity, population dynamics, mechanisms of divergence and adaptation and evolutionary change. However, the rate of image acquisition frequently outpaces our capacity to manually extract meaningful information from the images. Moreover, manual image analysis is low-throughput, difficult to reproduce, and typically measures only a few traits at a time. This has proven to be an impediment to the growing field of phenomics - the study of many phenotypic dimensions together. Computer vision (CV), the automated extraction and processing of information from digital images, is a way to alleviate this longstanding analytical bottleneck. In this review, we illustrate the capabilities of CV for fast, comprehensive, and reproducible image analysis in ecology and evolution. First, we briefly review phenomics, arguing that ecologists and evolutionary biologists can most effectively capture phenomic-level data by using CV. Next, we describe the primary types of image-based data, and review CV approaches for extracting them (including techniques that entail machine learning and others that do not). We identify common hurdles and pitfalls, and then highlight recent successful implementations of CV in the study of ecology and evolution. Finally, we outline promising future applications for CV in biology. We anticipate that CV will become a basic component of the biologist’s toolkit, further enhancing data quality and quantity, and sparking changes in how empirical ecological and evolutionary research will be conducted.

scholarly journals Customized Dictionary Learning for Subdatasets with Fine Granularity

2016 ◽  
Vol 2016 ◽  
pp. 1-13
Author(s):  
Lei Ye ◽  
Can Wang ◽  
Xin Xu ◽  
Hui Qian
Keyword(s):  
Machine Learning ◽  
Computer Vision ◽  
Theoretical Analysis ◽  
Improve Performance ◽  
Real World Data ◽  
Sparse Models ◽  
Learned Dictionary ◽  
Wide Range ◽  
Sparsity Constraints ◽  
The Difference

Sparse models have a wide range of applications in machine learning and computer vision. Using a learned dictionary instead of an “off-the-shelf” one can dramatically improve performance on a particular dataset. However, learning a new one for each subdataset (subject) with fine granularity may be unwarranted or impractical, due to restricted availability subdataset samples and tremendous numbers of subjects. To remedy this, we consider the dictionary customization problem, that is, specializing an existing global dictionary corresponding to the total dataset, with the aid of auxiliary samples obtained from the target subdataset. Inspired by observation and then deduced from theoretical analysis, a regularizer is employed penalizing the difference between the global and the customized dictionary. By minimizing the sum of reconstruction errors of the above regularizer under sparsity constraints, we exploit the characteristics of the target subdataset contained in the auxiliary samples while maintaining the basic sketches stored in the global dictionary. An efficient algorithm is presented and validated with experiments on real-world data.

scholarly journals Bayesian machine learning analysis of single-molecule fluorescence colocalization images

2021 ◽  
Author(s):  
Yerdos A. Ordabayev ◽  
Larry J. Friedman ◽  
Jeff Gelles ◽  
Douglas L. Theobald
Keyword(s):  
Machine Learning ◽  
Single Molecule ◽  
Specific Binding ◽  
Image Data ◽  
Automated Analysis ◽  
Surface Binding ◽  
Single Molecule Fluorescence ◽  
Binding Characteristics ◽  
Wide Range ◽  
Downstream Analysis

AbstractMulti-wavelength single-molecule fluorescence colocalization (CoSMoS) methods allow elucidation of complex biochemical reaction mechanisms. However, analysis of CoSMoS data is intrinsically challenging because of low image signal-to-noise ratios, non-specific surface binding of the fluorescent molecules, and analysis methods that require subjective inputs to achieve accurate results. Here, we use Bayesian probabilistic programming to implement Tapqir, an unsupervised machine learning method based on a holistic, physics-based causal model of CoSMoS data. This method accounts for uncertainties in image analysis due to photon and camera noise, optical non-uniformities, non-specific binding, and spot detection. Rather than merely producing a binary “spot/no spot” classification of unspecified reliability, Tapqir objectively assigns spot classification probabilities that allow accurate downstream analysis of molecular dynamics, thermodynamics, and kinetics. We both quantitatively validate Tapqir performance against simulated CoSMoS image data with known properties and also demonstrate that it implements fully objective, automated analysis of experiment-derived data sets with a wide range of signal, noise, and non-specific binding characteristics.

scholarly journals CNN-Based Illumination Estimation with Semantic Information

2020 ◽  
Vol 10 (14) ◽  
pp. 4806 ◽  
Author(s):  
Ho-Hyoung Choi ◽  
Hyun-Soo Kang ◽  
Byoung-Ju Yun
Keyword(s):  
Neural Network ◽  
Computer Vision ◽  
Semantic Information ◽  
Color Constancy ◽  
Noisy Data ◽  
Image Data ◽  
Input Image ◽  
The Novel ◽  
Image Patches ◽  
Wide Range

For more than a decade, both academia and industry have focused attention on the computer vision and in particular the computational color constancy (CVCC). The CVCC is used as a fundamental preprocessing task in a wide range of computer vision applications. While our human visual system (HVS) has the innate ability to perceive constant surface colors of objects under varying illumination spectra, the computer vision is facing the color constancy challenge in nature. Accordingly, this article proposes novel convolutional neural network (CNN) architecture based on the residual neural network which consists of pre-activation, atrous or dilated convolution and batch normalization. The proposed network can automatically decide what to learn from input image data and how to pool without supervision. When receiving input image data, the proposed network crops each image into image patches prior to training. Once the network begins learning, local semantic information is automatically extracted from the image patches and fed to its novel pooling layer. As a result of the semantic pooling, a weighted map or a mask is generated. Simultaneously, the extracted information is estimated and combined to form global information during training. The use of the novel pooling layer enables the proposed network to distinguish between useful data and noisy data, and thus efficiently remove noisy data during learning and evaluating. The main contribution of the proposed network is taking CVCC to higher accuracy and efficiency by adopting the novel pooling method. The experimental results demonstrate that the proposed network outperforms its conventional counterparts in estimation accuracy.

scholarly journals A Framework for the Image Retrieval System Based on Histogram Normalization Technique with Python

2020 ◽  
Vol 9 (4) ◽  
pp. 2300-2304
Keyword(s):  
Machine Learning ◽  
Computer Vision ◽  
Digital Images ◽  
Image Representation ◽  
Learning Model ◽  
Multimedia Data ◽  
Multimedia Content ◽  
Machine Learning Model ◽  
Image Retrieval System ◽  
Data Content

The processing of multimedia content is used for real-world computer vision in various applications, and digital images make up a large part of multimedia data. The processing of multimedia content is used for real-computer vision in various applications, and digital images make up a large part of multimedia data. Content-based Retrieval of photographs (CBIR) is a system of picture recovery which utilizes the visual highlights of a picture, for example, shading, shape and surface so as to look through the client based inquiry pictures from the huge databases. CBIR relies upon highlight extraction of a picture which are the visual highlights and these highlights are extricated naturally i.e. without human collaboration. We intend in this paper to provide a detailed overview of recent developments related to CBIR and image representation. We researched the main aspects of various models of image recovery and image representation from low-level feature extraction to recent semantict ML approaches. And, for extraction of features, HSV, image segmentation and color histogram techniques are used, which effectively gives us the main point in an image that these techniques are used to minimize complexity, expense, and energy and time consumption. Then a machine learning model is trained for similarity test and the validation and texting phases are performed accordingly which leads to better performance as. Then a machine learning model is trained for similarity testing and then the validation and texting steps are performed accordingly, resulting in improved results compared to previously performed techniques. The precision values in the proposed technique are fairly excellent.

Linguistic Indexing of Images with Database Mediation

2011 ◽  
pp. 2420-2425
Author(s):  
Emmanuel Udoh
Keyword(s):  
Machine Learning ◽  
Computer Vision ◽  
Object Recognition ◽  
Image Retrieval ◽  
Statistical Modeling ◽  
Digital Images ◽  
Statistical Error ◽  
Large Databases ◽  
Visual Aid ◽  
Active Research

Computer vision or object recognition complements human or biological vision using techniques from machine learning, statistics, scene reconstruction, indexing and event analysis. Object recognition is an active research area that implements artificial vision in software and hardware. Some application examples are autonomous robots, surveillance, indexing databases of pictures and human computer interaction. This visual aid is beneficial to users, because humans remember information with greater accuracy when it is presented visually than when it originates in writing, speech or in kinesthetic form. Linguistic indexing adds another dimension to computer vision by automatically assigning words or textual descriptions to images. This augments content-based image retrieval (CBIR) that extracts or searches for digital images in large databases. According to Li and Wang (2003), most of the existing CBIR projects are general-purpose image retrieval systems that search images visually similar to a query sketch. Current CBIR systems are incapable of assigning words automatically to images due to the inherent difficulty of recognizing numerous objects at once. This current situation is stimulating several research endeavors that seek to assign text to images, thereby improving image retrieval in large databases. To enhance information processing using object recognition techniques, current research has focused on automatic linguistic indexing of digital images (ALIDI). ALIDI requires a combination of mathematical, statistical, computational, and graphical backgrounds. Many researchers have focused on various aspects of linguistic processing such as CBIR (Ghosal, Ircing, & Khudanpur, 2005; Iqbal & Aggarwal, 2002, Wang, 2001) machine learning techniques (Iqbal & Aggarwal, 2002), digital library (Witen & Bainbridge, 2003) and statistical modeling (Li, Gray, & Olsen, 20004, Li & Wang, 2003). A growing approach is the utilization of statistical models as demonstrated by Li and Wang (2003). It entails building databases of images to be used for supervised learning. A trained system is used to recognize and identify new images with statistical error margin. This statistical modeling approach uses a hidden Markov model to extract representative information about any category of images analyzed. However, in using computer to recognize images with textual description, some of the researchers employ solely text-based approaches. In this article, the focus is on the computational and graphical aspects of ALIDI in a system that uses Web-based access in order to enable wider usage (Ntoulas, Chao, & Cho, 2005). This system uses image composition (primary hue and saturation) in the linguistic indexing of digital images or pictures.

Understanding the substrate specificity of conventional calpains

2012 ◽  
Vol 393 (9) ◽  
pp. 853-871 ◽  
Author(s):  
Hiroyuki Sorimachi ◽  
Hiroshi Mamitsuka ◽  
Yasuko Ono
Keyword(s):  
Machine Learning ◽  
Substrate Specificity ◽  
3D Structure ◽  
Limited Proteolysis ◽  
Cleavage Sites ◽  
Full Spectrum ◽  
Substrate Specificities ◽  
Biological Phenomena ◽  
Wide Range ◽  
Intracellular Ca

Abstract: Calpains are intracellular Ca2+-dependent Cys proteases that play important roles in a wide range of biological phenomena via the limited proteolysis of their substrates. Genetic defects in calpain genes cause lethality and/or functional deficits in many organisms, including humans. Despite their biological importance, the mechanisms underlying the action of calpains, particularly of their substrate specificities, remain largely unknown. Studies show that certain sequence preferences influence calpain substrate recognition, and some properties of amino acids have been related successfully to substrate specificity and to the calpains’ 3D structure. The full spectrum of this substrate specificity, however, has not been clarified using standard sequence analysis algorithms, e.g., the position-specific scoring-matrix method. More advanced bioinformatics techniques were used recently to identify the substrate specificities of calpains and to develop a predictor for calpain cleavage sites, demonstrating the potential of combining empirical data acquisition and machine learning. This review discusses the calpains’ substrate specificities, introducing the benefits of bioinformatics applications. In conclusion, machine learning has led to the development of useful predictors for calpain cleavage sites, although the accuracy of the predictions still needs improvement. Machine learning has also elucidated information about the properties of calpains’ substrate specificities, including a preference for sequences over secondary structures and the existence of a substrate specificity difference between two similar conventional calpains, which has never been indicated biochemically.

scholarly journals A cost-effective maize ear phenotyping platform enables rapid categorization and quantification of kernels

2020 ◽  
Author(s):  
Cedar Warman ◽  
Christopher M. Sullivan ◽  
Justin Preece ◽  
Michaela E. Buchanan ◽  
Zuzana Vejlupkova ◽  
...  
Keyword(s):  
Computer Vision ◽  
Deep Learning ◽  
Low Cost ◽  
Digital Camera ◽  
Cost Effective ◽  
Detection Model ◽  
Biological Phenomena ◽  
Effective Combination ◽  
Wide Range ◽  
Maize Ear

AbstractHigh-throughput phenotyping systems are powerful, dramatically changing our ability to document, measure, and detect biological phenomena. Here, we describe a cost-effective combination of a custom-built imaging platform and deep-learning-based computer vision pipeline. A minimal version of the maize ear scanner was built with low-cost and readily available parts. The scanner rotates a maize ear while a cellphone or digital camera captures a video of the surface of the ear. Videos are then digitally flattened into two-dimensional ear projections. Segregating GFP and anthocyanin kernel phenotype are clearly distinguishable in ear projections, and can be manually annotated using image analysis software. Increased throughput was attained by designing and implementing an automated kernel counting system using transfer learning and a deep learning object detection model. The computer vision model was able to rapidly assess over 390,000 kernels, identifying male-specific transmission defects across a wide range of GFP-marked mutant alleles. This includes a previously undescribed defect putatively associated with mutation of Zm00001d002824, a gene predicted to encode a vacuolar processing enzyme (VPE). We show that by using this system, the quantification of transmission data and other ear phenotypes can be accelerated and scaled to generate large datasets for robust analyses.One sentence summaryA maize ear phenotyping system built from commonly available parts creates images of the surface of ears and identifies kernel phenotypes with a deep-learning-based computer vision pipeline.

Application-oriented robotic vision – a review

Robotica ◽  
1984 ◽  
Vol 2 (1) ◽  
pp. 3-15 ◽  
Author(s):  
R. A. Jarvis
Keyword(s):  
Computer Vision ◽  
High Speed ◽  
Image Data ◽  
Vision Systems ◽  
Levels Of Abstraction ◽  
Biological Vision ◽  
Robotic Vision ◽  
Machine Perception ◽  
Wide Range ◽  
Industrial Operations

SUMMARYComputer Vision is essentially concerned with emulating the process of seeing, naturally manifested in various higher biological systems,1–4 on a computational apparatus, and is consequently part of the Artificial Intelligence field within the sub-category of Machine perception. Seeing has to do with making sense of image data acquired through an optical system and subsequently dealt with at increasing levels of abstraction and association with known facts about the world. The spectrum of interest in Computer Vision ranges from attempting to answer basic questions concerning the functionality of biological vision systems, particularly human, at one end, all the way to enhancing the reliability, speed and cost effectiveness of specific industrial operations, particularly component inspection and vision driven robotic manipulation. The main bulk of interest is in the middle, where the quest for generality pushes interest towards biological vision systems with their demonstrated effectiveness in a wide range of environments, some hostile, whilst the need for economic viability and timeliness in relation to particular application pushes interest towards finding workable algorithms which function reliably at high speed on affordable apparatus.This paper is addressed, in somewhat tutorial style, at clarifying, by examples of work in the area, the issues surrounding application oriented robotic vision systems, their assumptions, strengths, weaknesses and degree of generality, and at the same time putting them in the context of the overall field of Computer Vision. In addition, the paper points to directions of development which promise to provide powerful industrial vision tools at an acceptable price.

Image classification with quantum pre-training and auto-encoders

2018 ◽  
Vol 16 (08) ◽  
pp. 1840009 ◽  
Author(s):  
Sebastien Piat ◽  
Nairi Usher ◽  
Simone Severini ◽  
Mark Herbster ◽  
Tommaso Mansi ◽  
...  
Keyword(s):  
Machine Learning ◽  
Computer Vision ◽  
Image Classification ◽  
Large Scale ◽  
Medical Image Analysis ◽  
Learning Approaches ◽  
Quantum Devices ◽  
Main Challenge ◽  
Small Quantum ◽  
Wide Range

Computer vision has a wide range of applications from medical image analysis to robotics. Over the past few years, the field has been transformed by machine learning and stands to benefit from potential advances in quantum computing. The main challenge for processing images on current and near-term quantum devices is the size of the data such devices can process. Images can be large, multidimensional and have multiple color channels. Current machine learning approaches to computer vision that exploit quantum resources require a significant amount of manual pre-processing of the images in order to be able to fit them onto the device. This paper proposes a framework to address the problem of processing large scale data on small quantum devices. This framework does not require any dataset-specific processing or information and works on large, grayscale and RGB images. Furthermore, it is capable of scaling to larger quantum hardware architectures as they become available. In the proposed approach, a classical autoencoder is trained to compress the image data to a size that can be loaded onto a quantum device. Then, a Restricted Boltzmann Machine (RBM) is trained on the D-Wave device using the compressed data, and the weights from the RBM are then used to initialize a neural network for image classification. Results are demonstrated on two MNIST datasets and two medical imaging datasets.

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